Author: bugman
Date: Fri Mar 22 16:56:08 2013
New Revision: 18986
URL: http://svn.gna.org/viewcvs/relax?rev=18986&view=rev
Log:
Next block of the manual merger of the frame_order_testing branch.
The commands used were:
svn merge -r18001:18002
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
svn merge -r18002:18003
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
svn merge -r18003:18004
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
svn merge -r18004:18005
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
svn merge -r18005:18006
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
svn merge -r18006:18007
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
svn merge -r18007:18008
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
svn merge -r18008:18009
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
svn merge -r18009:18010
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
The console messages were:
[edau@localhost relax-trunk]$ svn merge -r18001:18002
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
--- Merging r18002 into '.':
U specific_fns/frame_order.py
[edau@localhost relax-trunk]$ svn merge -r18002:18003
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
--- Merging r18003 into '.':
G specific_fns/frame_order.py
[edau@localhost relax-trunk]$ svn merge -r18003:18004
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
--- Merging r18004 into '.':
A test_suite/shared_data/frame_order/cam/full_analysis.py
[edau@localhost relax-trunk]$ svn merge -r18004:18005
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
--- Merging r18005 into '.':
U auto_analyses/frame_order.py
[edau@localhost relax-trunk]$ svn merge -r18005:18006
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
--- Merging r18006 into '.':
G auto_analyses/frame_order.py
[edau@localhost relax-trunk]$ svn merge -r18006:18007
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
--- Merging r18007 into '.':
G auto_analyses/frame_order.py
[edau@localhost relax-trunk]$ svn merge -r18007:18008
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
--- Merging r18008 into '.':
G auto_analyses/frame_order.py
[edau@localhost relax-trunk]$ svn merge -r18008:18009
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
--- Merging r18009 into '.':
G auto_analyses/frame_order.py
[edau@localhost relax-trunk]$ svn merge -r18009:18010
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
--- Merging r18010 into '.':
G auto_analyses/frame_order.py
[edau@localhost relax-trunk]$
Added:
trunk/test_suite/shared_data/frame_order/cam/full_analysis.py
- copied unchanged from r18004,
branches/frame_order_testing/test_suite/shared_data/frame_order/cam/full_analysis.py
Modified:
trunk/auto_analyses/frame_order.py
trunk/specific_fns/frame_order.py
Modified: trunk/auto_analyses/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/auto_analyses/frame_order.py?rev=18986&r1=18985&r2=18986&view=diff
==============================================================================
--- trunk/auto_analyses/frame_order.py (original)
+++ trunk/auto_analyses/frame_order.py Fri Mar 22 16:56:08 2013
@@ -42,25 +42,41 @@
class Frame_order_analysis:
- def __init__(self, data_pipe_full=None, data_pipe_subset=None,
pipe_bundle=None, results_dir=None, grid_inc=11, grid_inc_rigid=21,
min_algor='simplex', num_int_pts_grid=50, num_int_pts_subset=[20, 100],
num_int_pts_full=[100, 1000, 200000], mc_sim_num=500):
+ """The frame order auto-analysis protocol."""
+
+ def __init__(self, data_pipe_full=None, data_pipe_subset=None,
pipe_bundle=None, results_dir=None, grid_inc=11, grid_inc_rigid=21,
min_algor='simplex', num_int_pts_grid=50, num_int_pts_subset=[20, 100],
func_tol_subset=[1e-2, 1e-2], num_int_pts_full=[100, 1000, 200000],
func_tol_full=[1e-2, 1e-3, 1e-4], mc_sim_num=500, mc_int_pts=1000,
mc_func_tol=1e-3):
"""Perform the full frame order analysis.
- @param data_pipe_full: The name of the data pipe containing all
of the RDC and PCS data.
- @type data_pipe_full: str
- @param data_pipe_subset: The name of the data pipe containing all
of the RDC data but only a small subset of ~5 PCS points.
- @type data_pipe_subset: str
- @keyword pipe_bundle: The data pipe bundle to associate all
spawned data pipes with.
- @type pipe_bundle: str
- @keyword results_dir: The directory where files are saved in.
- @type results_dir: str
- @keyword grid_inc: The number of grid increments to use in
the grid search of certain models.
- @type grid_inc: int
- @keyword grid_inc_rigid: The number of grid increments to use in
the grid search of the initial rigid model.
- @type grid_inc_rigid: int
- @keyword min_algor: The minimisation algorithm (in most
cases this should not be changed).
- @type min_algor: str
- @keyword mc_sim_num: The number of Monte Carlo simulations to
be used for error analysis at the end of the analysis.
- @type mc_sim_num: int
+ @param data_pipe_full: The name of the data pipe containing
all of the RDC and PCS data.
+ @type data_pipe_full: str
+ @param data_pipe_subset: The name of the data pipe containing
all of the RDC data but only a small subset of ~5 PCS points.
+ @type data_pipe_subset: str
+ @keyword pipe_bundle: The data pipe bundle to associate
all spawned data pipes with.
+ @type pipe_bundle: str
+ @keyword results_dir: The directory where files are saved
in.
+ @type results_dir: str
+ @keyword grid_inc: The number of grid increments to use
in the grid search of certain models.
+ @type grid_inc: int
+ @keyword grid_inc_rigid: The number of grid increments to use
in the grid search of the initial rigid model.
+ @type grid_inc_rigid: int
+ @keyword min_algor: The minimisation algorithm (in most
cases this should not be changed).
+ @type min_algor: str
+ @keyword num_int_pts_grid: The number of Sobol' points for the
PCS numerical integration in the grid searches.
+ @type num_int_pts_grid: int
+ @keyword num_int_pts_subset: The list of the number of Sobol'
points for the PCS numerical integration to use iteratively in the
optimisations after the grid search (for the PCS data subset).
+ @type num_int_pts_subset: list of int
+ @keyword func_tol_subset: The minimisation function tolerance
cutoff to terminate optimisation (for the PCS data subset, see the minimise
user function).
+ @type func_tol_subset: list of float
+ @keyword num_int_pts_full: The list of the number of Sobol'
points for the PCS numerical integration to use iteratively in the
optimisations after the grid search (for all PCS and RDC data).
+ @type num_int_pts_full: list of int
+ @keyword func_tol_full: The minimisation function tolerance
cutoff to terminate optimisation (for all PCS and RDC data, see the minimise
user function).
+ @type func_tol_full: list of float
+ @keyword mc_sim_num: The number of Monte Carlo
simulations to be used for error analysis at the end of the analysis.
+ @type mc_sim_num: int
+ @keyword mc_int_num: The number of Sobol' points for the
PCS numerical integration during Monte Carlo simulations.
+ @type mc_int_num: int
+ @keyword mc_func_tol: The minimisation function tolerance
cutoff to terminate optimisation during Monte Carlo simulations.
+ @type mc_func_tol: float
"""
# Execution lock.
@@ -75,8 +91,12 @@
self.min_algor = min_algor
self.num_int_pts_grid = num_int_pts_grid
self.num_int_pts_subset = num_int_pts_subset
+ self.func_tol_subset = func_tol_subset
self.num_int_pts_full = num_int_pts_full
+ self.func_tol_full = func_tol_full
self.mc_sim_num = mc_sim_num
+ self.mc_int_pts = mc_int_pts
+ self.mc_func_tol = mc_func_tol
# A dictionary of the data pipe names.
self.models = {}
@@ -104,11 +124,14 @@
# Model selection.
self.interpreter.model_selection(method='AIC',
modsel_pipe='final', pipes=self.pipes)
+ # The number of integration points.
+ self.interpreter.frame_order.num_int_pts(num=self.mc_int_pts)
+
# Monte Carlo simulations.
self.interpreter.monte_carlo.setup(number=self.mc_sim_num)
self.interpreter.monte_carlo.create_data()
self.interpreter.monte_carlo.initial_values()
- self.interpreter.minimise(self.min_algor, constraints=False)
+ self.interpreter.minimise(self.min_algor,
func_tol=self.mc_func_tol, constraints=False)
self.interpreter.eliminate()
self.interpreter.monte_carlo.error_analysis()
@@ -131,13 +154,39 @@
if not isinstance(self.pipe_bundle, str):
raise RelaxError("The pipe bundle name '%s' is invalid." %
self.pipe_bundle)
- # Min vars.
+ # Minimisation variables.
if not isinstance(self.grid_inc, int):
raise RelaxError("The grid_inc user variable '%s' is incorrectly
set. It should be an integer." % self.grid_inc)
+ if not isinstance(self.grid_inc_rigid, int):
+ raise RelaxError("The grid_inc_rigid user variable '%s' is
incorrectly set. It should be an integer." % self.grid_inc)
if not isinstance(self.min_algor, str):
raise RelaxError("The min_algor user variable '%s' is
incorrectly set. It should be a string." % self.min_algor)
+ if not isinstance(self.num_int_pts_grid, int):
+ raise RelaxError("The num_int_pts_grid user variable '%s' is
incorrectly set. It should be an integer." % self.mc_sim_num)
if not isinstance(self.mc_sim_num, int):
raise RelaxError("The mc_sim_num user variable '%s' is
incorrectly set. It should be an integer." % self.mc_sim_num)
+ if not isinstance(self.mc_int_pts, int):
+ raise RelaxError("The mc_int_pts user variable '%s' is
incorrectly set. It should be an integer." % self.mc_int_pts)
+ if not isinstance(self.mc_func_tol, float):
+ raise RelaxError("The mc_func_tol user variable '%s' is
incorrectly set. It should be a floating point number." % self.mc_func_tol)
+
+ # Zooming minimisation (PCS subset).
+ if len(self.num_int_pts_subset) != len(self.func_tol_subset):
+ raise RelaxError("The num_int_pts_subset and func_tol_subset
user variables of '%s' and '%s' respectively must be of the same length." %
(self.num_int_pts_subset, self.func_tol_subset))
+ for i in range(len(self.num_int_pts_subset)):
+ if not isinstance(self.num_int_pts_subset[i], int):
+ raise RelaxError("The num_int_pts_subset user variable '%s'
must be a list of integers." % self.num_int_pts_subset)
+ if not isinstance(self.func_tol_subset[i], float):
+ raise RelaxError("The func_tol_subset user variable '%s'
must be a list of floats." % self.func_tol_subset)
+
+ # Zooming minimisation (all RDC and PCS data).
+ if len(self.num_int_pts_full) != len(self.func_tol_full):
+ raise RelaxError("The num_int_pts_full and func_tol_full user
variables of '%s' and '%s' respectively must be of the same length." %
(self.num_int_pts_full, self.func_tol_full))
+ for i in range(len(self.num_int_pts_full)):
+ if not isinstance(self.num_int_pts_full[i], int):
+ raise RelaxError("The num_int_pts_full user variable '%s'
must be a list of integers." % self.num_int_pts_full)
+ if not isinstance(self.func_tol_full[i], float):
+ raise RelaxError("The func_tol_full user variable '%s' must
be a list of floats." % self.func_tol_full)
def custom_grid_incs(self, model):
@@ -280,17 +329,17 @@
self.interpreter.grid_search(inc=incs, constraints=False)
# Minimise (for the PCS data subset and full RDC set).
- for num in self.num_int_pts_subset:
- self.interpreter.frame_order.num_int_pts(num=num)
- self.interpreter.minimise(self.min_algor, constraints=False)
+ for i in range(len(self.num_int_pts_subset)):
+
self.interpreter.frame_order.num_int_pts(num=self.num_int_pts_subset[i])
+ self.interpreter.minimise(self.min_algor,
func_tol=self.func_tol_subset[i], constraints=False)
# Copy the PCS data.
self.interpreter.pcs.copy(pipe_from=self.data_pipe_full,
pipe_to=self.models[model])
# Minimise (for the full data set).
- for num in self.num_int_pts_full:
- self.interpreter.frame_order.num_int_pts(num=num)
- self.interpreter.minimise(self.min_algor, constraints=False)
+ for i in range(len(self.num_int_pts_full)):
+
self.interpreter.frame_order.num_int_pts(num=self.num_int_pts_full[i])
+ self.interpreter.minimise(self.min_algor,
func_tol=self.func_tol_full[i], constraints=False)
# Results printout.
self.print_results()
Modified: trunk/specific_fns/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/specific_fns/frame_order.py?rev=18986&r1=18985&r2=18986&view=diff
==============================================================================
--- trunk/specific_fns/frame_order.py (original)
+++ trunk/specific_fns/frame_order.py Fri Mar 22 16:56:08 2013
@@ -1660,6 +1660,29 @@
cdp.select = False
+ def duplicate_data(self, pipe_from=None, pipe_to=None, model_info=None,
global_stats=False, verbose=True):
+ """Duplicate the data specific to a single frame order data pipe.
+
+ @keyword pipe_from: The data pipe to copy the data from.
+ @type pipe_from: str
+ @keyword pipe_to: The data pipe to copy the data to.
+ @type pipe_to: str
+ @param model_info: The model index from model_loop().
+ @type model_info: int
+ @keyword global_stats: The global statistics flag.
+ @type global_stats: bool
+ @keyword verbose: Unused.
+ @type verbose: bool
+ """
+
+ # Check that the data pipe does not exist.
+ if pipes.has_pipe(pipe_to):
+ raise RelaxError("The data pipe '%s' already exists." % pipe_to)
+
+ # Create the pipe_to data pipe by copying.
+ pipes.copy(pipe_from=pipe_from, pipe_to=pipe_to)
+
+
def eliminate(self, name, value, model_info, args, sim=None):
"""Model elimination method.
@@ -2170,6 +2193,10 @@
# Loop over the residue specific parameters.
for param in self.data_names(set='params'):
+ # Not a parameter of the model.
+ if param not in cdp.params:
+ continue
+
# Return the parameter array.
if index == inc:
setattr(cdp, param + "_err", error)
@@ -2215,6 +2242,10 @@
# Loop over all the parameter names.
for object_name in param_names:
+ # Not a parameter of the model.
+ if object_name not in cdp.params:
+ continue
+
# Name for the simulation object.
sim_object_name = object_name + '_sim'
@@ -2228,8 +2259,8 @@
# Loop over all the data names.
for object_name in param_names:
- # Skip non-existent objects.
- if not hasattr(cdp, object_name):
+ # Not a parameter of the model.
+ if object_name not in cdp.params:
continue
# Name for the simulation object.
@@ -2324,8 +2355,8 @@
# Loop over the parameters.
for param in param_names:
- # Skip non-existent objects.
- if not hasattr(cdp, param):
+ # Not a parameter of the model.
+ if param not in cdp.params:
continue
# Return the parameter array.
r18986 - in /trunk: auto_analyses/ specific_fns/ test_suite/shared_data/frame_order/cam/